Aton alongside other Nativs find Kya unconscious, in The Roots. Aton tries to warn Kya, she must wake up, as they are being chased by a bunch of Wolfen. Eventually he leads her to safety, and the two team up to defeat a Wolfen guarding the entrance to Nativ City. Aton devises a plan to knock out the Wolfen, by using Kya as bait. In order for the plan to work, Kya must obtain the attention of the Wolfen and have it follow her to an area with a giant X on the ground. Once past the X, Aton will release two giant logs that will smash the Wolfen unconscious. Upon the completion of the plan, Aton takes the knocked out Wolfen along with Kya, to Nativ City. He talks to her about his village, which is a hidden location from the Wolfen. Unfortunately, any Nativ that leaves the village get captured by the Wolfen. He introduces Kya to Atea, the village elder of the City. Atea sees great promise in Kya, and despite Aton's lack of trust, Atea allows for Kya to learn new abilities to help find her brother Frank. Aton acts as Kya's guide until she meets Stuff, he leaves signs for her around Nativ City, so she can go to the Flying Forest and retrieve the Blue Egg.
After Kya retrieves the Receptacle, Atea and Area, go to the Hunters Domain. Atea is then captured by The Hunter, while Area ran away. When Kya gets back to Nativ City, in search for a Jamgut call, she bumps into Aton and Area arguing. Aton is furious that Area would leave an old man alone to fend for himself, Kya volunteers herself to help save Atea, but Aton believes she's done enough already. Kya won't take no for an answer, she is going to save Atea no matter what anyone says; much to Aton's dismay.

Aton assists Kya at first, but later decides to contact Brazul to make a deal. Aton will trick Kya into meeting Brazul if he gives his word not to harm the Nativs. Aton holds up his end of the bargain and guides Kya right to Brazul at the Amber Quarry. Brazul, however, betrays Aton by using him to locate Nativ City and ordering his Wolfen to attack. Aton disappears after this cut scene and the battle between Kya and Brazul that follows. His whereabouts are unknown until one of the last boss battles.

In the end of the game, Kya meets Aton again as a Wolfen. They fight and Kya knocks him out, but she cannot exorcise him. The room fills with lava shortly after, killing him.